I can't be sure it's related but after I turned on File Encryption Spotlight just stopped working on files folders and apps. I tried all the advice I saw in this post on this forum and more, including reinstalling the OS and resetting parameter RAM and deleting the .Spotlight-V100 folder.
I found the answer today and it took so long I thought it was worth posting both the question and the answer here.
I found the answer on this post in an Apple Community forum.
The key was to rebuild the Launch Services Database - I didn’t even know that was a thing. You need to use the terminal and run this command:
sudo /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -kill -r -domain u -domain s -domain l -v
Takes a minute or so to complete and you get a lot of lines with errors. Then I continued with the advice in the post to rebuild the indexing with the following
sudo mdutil -i on /
sudo mdutil -E /
After running for just a few minutes I started to see apps show back up in Spotlight.
Hope I can save someone else a few weeks of pain and searching.